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....Paired-End reAd mergeR....

Authors: Jiajie Zhang, Kassian Kobert, Tomas Flouri, Alexandros Stamatakis

License: Creative Commons license
                with
Attribution-NonCommercial-ShareAlike 3.0 Unported

Introduction:
-------------
PEAR  assembles  Illumina paired-end reads if the DNA fragment sizes are smaller
than  twice  the length of reads. PEAR can assemble 95% of reads with 35-bp mean
overlap  with  a  false-positive rate of 0.004. PEAR also works with multiplexed
data  sets  where  the  true  underlying  DNA  fragment size varies. PEAR has an
extremely low false-positive rate of 0.0003 on data sets where no overlap exists
between  the  two  reads (i.e. when DNA fragment sizes are larger than twice the
read length).

For more information, requests and bug-reports visit our website at 

                http://www.exelixis-lab.org/web/software/pear

Requirements:
-------------
PEAR  requires  the  autotools build system and libtool in order to proceed with
the  installation  steps. In case you do not have autotools and libtool, you can
install them using the command:

sudo apt-get install build-essential autoconf automake libtool

Additionally, if  you would like to compile bzip2 support in PEAR, you will need
to  have  bzlib installed on your system before installing PEAR. You can install
it with:

sudo apt-get install libbz2-dev

How to compile:
---------------
1. git clone https://github.com/xflouris/PEAR.git
2. cd PEAR
3. ./autogen.sh
4. ./configure
5. make
6. sudo make install

How to run self-tests:
----------------------
1. Make sure you have python 2.4 (or newer) installed
2. Go to the "test" folder
3. type: ./test.py

This  will run PEAR on several simulated data sets with various options to check
if the newly compiled program works properly.

How to use:
-----------
PEAR  can  robustly  assemble most of the data sets with default parameters. The
basic command to run PEAR is

  ./pear -f forward_read.fastq -r reverse_read.fastq -o output_prefix

The forward_read file usually has "R1" in the name, and the reverse_read
file usually has "R2" in the name.

Output files:
-------------
PEAR produces 4 output files:

1. output_prefix.assembled.fastq - the assembled pairs
2. output_prefix.unassembled.forward.fastq - unassembled forward reads
3. output_prefix.unassembled.reverse.fastq - unassembled reverse reads
4. output_prefix.dicarded.fastq  - reads which did not meet criteria specified in options

Advanced usage:
---------------

For further options and fine-tuning type
  
  ./pear -h  

Important information:
----------------------
1. The input files must be in FASTQ format
2. PEAR  does not check the paired-end reads names. PEAR assumes that the reads
in  both files are in the same flowcell position if they appear on the same line
number.  Therefore,  the  validity  of  the  input  files  is  left  as  a  user
responsibility.

How to cite:
------------
J. Zhang, K. Kobert, T. Flouri, A. Stamatakis. PEAR: A fast and accurate Illumina
Paired-End reAd mergeR. Bioinformatics 30(5): 614-620, 2014.